#!/usr/bin/env python3
"""Module containing the Pdb2gmx class and the command line interface."""
import os
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_md.gromacs.common import get_gromacs_version
from biobb_md.gromacs.common import GromacsVersionError
[docs]class Pdb2gmx(BiobbObject):
"""
| biobb_md Pdb2gmx
| Wrapper class for the `GROMACS pdb2gmx <http://manual.gromacs.org/current/onlinehelp/gmx-pdb2gmx.html>`_ module.
| The GROMACS pdb2gmx module, reads a .pdb (or .gro) file, reads some database files, adds hydrogens to the molecules and generates coordinates in GROMACS (GROMOS), or optionally .pdb, format and a topology in GROMACS format. These files can subsequently be processed to generate a run input file.
Args:
input_pdb_path (str): Path to the input PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs/egfr.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_gro_path (str): Path to the output GRO file. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_pdb2gmx.gro>`_. Accepted formats: gro (edam:format_2033).
output_top_zip_path (str): Path the output TOP topology in zip format. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_pdb2gmx.zip>`_. Accepted formats: zip (edam:format_3987).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **water_type** (*str*) - ("spce") Water molecule type. Values: spc, spce, tip3p, tip4p, tip5p, tips3p.
* **force_field** (*str*) - ("amber99sb-ildn") Force field to be used during the conversion. Values: gromos45a3, charmm27, gromos53a6, amber96, amber99, gromos43a2, gromos54a7, gromos43a1, amberGS, gromos53a5, amber99sb, amber03, amber99sb-ildn, oplsaa, amber94, amber99sb-star-ildn-mut.
* **ignh** (*bool*) - (False) Should pdb2gmx ignore the hidrogens in the original structure.
* **his** (*str*) - (None) Histidine protonation array.
* **merge** (*bool*) - (False) Merge all chains into a single molecule.
* **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
* **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **container_path** (*str*) - (None) Path to the binary executable of your container.
* **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
* **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
* **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
* **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
* **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
Examples:
This is a use example of how to use the building block from Python::
from biobb_md.gromacs.pdb2gmx import pdb2gmx
prop = { 'his': '0 0 1 1 0 0 0' }
pdb2gmx(input_pdb_path='/path/to/myStructure.pdb',
output_gro_path='/path/to/newStructure.gro',
output_top_zip_path='/path/to/newTopology.zip',
properties=prop)
Info:
* wrapped_software:
* name: GROMACS Pdb2gmx
* version: >5.1
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_pdb_path: str, output_gro_path: str, output_top_zip_path: str, properties: dict = None,
**kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
# Input/Output files
self.io_dict = {
"in": {"input_pdb_path": input_pdb_path},
"out": {"output_gro_path": output_gro_path, "output_top_zip_path": output_top_zip_path}
}
# Properties specific for BB
self.internal_top_name = properties.get('internal_top_name', 'p2g.top') # Excluded from documentation for simplicity
self.internal_itp_name = properties.get('internal_itp_name', 'posre.itp') # Excluded from documentation for simplicity
self.water_type = properties.get('water_type', 'spce')
self.force_field = properties.get('force_field', 'amber99sb-ildn')
self.ignh = properties.get('ignh', False)
self.his = properties.get('his', None)
self.merge = properties.get('merge', False)
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Check the properties
self.check_properties(properties)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`Pdb2gmx <gromacs.pdb2gmx.Pdb2gmx>` object."""
# Setup Biobb
if self.check_restart(): return 0
self.stage_files()
internal_top_name = fu.create_name(prefix=self.prefix, step=self.step, name=self.internal_top_name)
internal_itp_name = fu.create_name(prefix=self.prefix, step=self.step, name=self.internal_itp_name)
# Create command line
self.cmd = [self.gmx_path, "pdb2gmx",
"-f", self.stage_io_dict["in"]["input_pdb_path"],
"-o", self.stage_io_dict["out"]["output_gro_path"],
"-p", internal_top_name,
"-water", self.water_type,
"-ff", self.force_field,
"-i", internal_itp_name]
if self.his:
self.cmd.append("-his")
self.cmd = ['echo', self.his, '|'] + self.cmd
if self.ignh:
self.cmd.append("-ignh")
if self.merge:
self.cmd.append("-merge")
self.cmd.append("all")
if self.gmx_lib:
self.environment = os.environ.copy()
self.environment['GMXLIB'] = self.gmx_lib
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError("Gromacs version should be 5.1.2 or newer %d detected" % self.gmx_version)
fu.log("GROMACS %s %d version detected" % (self.__class__.__name__, self.gmx_version), self.out_log)
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
if self.container_path:
internal_top_name = os.path.join(self.stage_io_dict.get("unique_dir"), internal_top_name)
# zip topology
fu.log('Compressing topology to: %s' % self.io_dict["out"]["output_top_zip_path"], self.out_log,
self.global_log)
fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"], top_file=internal_top_name, out_log=self.out_log)
# Remove temporal files
self.tmp_files.extend([self.internal_top_name, self.internal_itp_name, self.stage_io_dict.get("unique_dir")])
self.remove_tmp_files()
return self.return_code
[docs]def pdb2gmx(input_pdb_path: str, output_gro_path: str, output_top_zip_path: str,
properties: dict = None, **kwargs) -> int:
"""Create :class:`Pdb2gmx <gromacs.pdb2gmx.Pdb2gmx>` class and
execute the :meth:`launch() <gromacs.pdb2gmx.Pdb2gmx.launch>` method."""
return Pdb2gmx(input_pdb_path=input_pdb_path, output_gro_path=output_gro_path,
output_top_zip_path=output_top_zip_path, properties=properties,
**kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Wrapper of the GROMACS pdb2gmx module.",
formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_pdb_path', required=True)
required_args.add_argument('--output_gro_path', required=True)
required_args.add_argument('--output_top_zip_path', required=True)
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call of each building block
pdb2gmx(input_pdb_path=args.input_pdb_path, output_gro_path=args.output_gro_path,
output_top_zip_path=args.output_top_zip_path, properties=properties)
if __name__ == '__main__':
main()